My $$ is on your R-09's input jack finally flaking out.
Unfortunately that seems to be the most likely cause of your problem. You can probably rule out problems with the mics or preamp if the gear sounds fine through one of your R09 input jacks but not the other. I assume you are using line in with your preamp. If so, you could set the pre at unity gain (11:00) so it acts as a battery box and see if you have the same problem going mic in.
Then if it still seems to be an issue with one of the R-09 jacks, it might be worth checking to be sure that the R-09's input jack isn't simply dirty (although I don't really think that's the problem from the issues you describe).
Guysonic has given the following advice:
Clean & recondition noisy mic. jacks with 91 - 99% pure isopropyl alcohol. Repeatedly insert a headphone type plug soaked to the point of dripping (filling the alcohol bottle cap and dipping only the metal part of the mini-plug works well) into the mic. jack until any connection noise disappears. Monitor the progress with a set of headphones while the deck is in a record function. Rotating the microphones plug should not produce audible noise with cleaned and conditioned contacts. Applying a contact conditioner to already cleaned plug and jack metal parts (Stereo retailer & Sonic Studios available Pro-Gold by Caig Labs works great) once to several times a year will help protect contacts from corrosion/wear and from producing noise for much longer between cleanings. (Return to Tapers Tips Page)
CAUTION ADVISED: AVOID PLACING CONTACT CLEANER ON ANYTHING BUT THE METAL CONNECTOR PARTS; Plastics can be softened, discolored, and even dissolved! This may actually coat the very metal contacts intended for cleaning! Fortunately, deck input jacks are reasonably resistant to alcohol and most ‘plastic safe’ cleaners when used occasionally and with care.
WARNING: Never spray anything into the jacks on a deck. Most Mini-DECK jacks are not the enclosed type anymore, but are open, allowing sprays to go where they can cause mechanical problems with the tape transport mechanisms and coat the tape.